HPRA CEO Lorraine Nolan told members of the Oireachtas Health Committee that the authority could not recommend widespread access to cannabis for the treatment of a range of medical conditions.
However, Ms Nolan said that access could be facilitated under appropriately-controlled circumstances where adequate assurance of patient safety and follow-up can be provided.
The HPRA provided an expert report to Minister for Health Simon Harris on the use of medicinal cannabis following cross-party support for legislation proposed by AAA-PBP TD Gino Kenny.
The HPRA specified three conditions that could be part of a monitored pilot programme: spasticity associated with MS, intractable nausea and vomiting associated with chemotherapy, and severe, treatment-resistant epilepsy.
Ms Nolan said that to date there is an absence of scientific data demonstrating the effectiveness and safety of cannabis products.
"There is insufficient information on the treatment of long-term medical conditions, such as those for which there is a public focus.
"In addition, most cannabis products available under international access schemes do not meet pharmaceutical quality requirements for medicines," Ms Nolan told members.
She also said the review highlighted significant gaps between the public perception of effectiveness and safety, and the regulatory requirement for scientific data which is mandatory to determine the role of cannabis as a medicine.
The HPRA report concluded that cannabis for medical use should only be initiated as part of a structured process of formal on-going clinical evaluation in patients with the clearly defined medical conditions.
This position is based on current scientific evidence and will be kept under review.
The Principal Officer of the Department of Health told the committee that the minister described the HPRA report as a "milestone" in the development of policy on medicinal cannabis.
Eugene Lennon also told members that patients accessing the proposed programme would be required to be under the care of a medical consultant.
"The minister intends to progress the establishment of this access programme as a priority. But to be clear, patients accessing cannabis under the programme, will need to be recommended for cannabis treatment by a relevant medical consultant involved in the patient's care," Mr Lennon said.
He also said that officials were examining legislation required to underpin the programme.
The committee was told that 40 countries were surveyed in the expert report. In Europe, 16 countries do not have any access programmes, nine have programmes for exceptional use similar to that advised by the HPRA, and three countries have wider access programmes.
Mr Lennon confirmed to Sinn Féin deputy Johnathan O'Brien that one licence had been already been granted to a patient for access to medicinal cannabis, while a second application had not been granted.